Construction of near-optimal vertex clique covering for real-world networks

We propose a method based on combining a constructive and a bounding heuristic to solve the vertex clique covering problem (CCP), where the aim is to partition the vertices of a graph into the smallest number of classes, which induce cliques. Searching for the solution to CCP is highly motivated by analysis of social and other real-world networks, applications in graph mining, as well as by the fact that CCP is one of the classical NP-hard problems. Combining the construction and the bounding heuristic helped us not only to find high-quality clique coverings but also to determine that in the domain of real-world networks, many of the obtained solutions are optimal, while the rest of them are near-optimal. In addition, the method has a polynomial time complexity and shows much promise for its practical use. Experimental results are presented for a fairly representative benchmark of real-world data. Our test graphs include extracts of web-based social networks, including some very large ones, several well-known graphs from network science, as well as coappearance networks of literary works' characters from the DIMACS graph coloring benchmark. We also present results for synthetic pseudorandom graphs structured according to the Erdös-Renyi model and Leighton's model

Construction of Near-Optimal Vertex Clique Covering for Real-World Networks

We propose a method based on combining a constructive and a bounding heuristic to solve the vertex clique covering problem (CCP), where the aim is to partition the vertices of a graph into the smallest number of classes, which induce cliques. Searching for the solution to CCP is highly motivated by analysis of social and other real-world networks, applications in graph mining, as well as by the fact that CCP is one of the classical NP-hard problems. Combining the construction and the bounding heuristic helped us not only to find high-quality clique coverings but also to determine that in the domain of real-world networks, many of the obtained solutions are optimal, while the rest of them are near-optimal. In addition, the method has a polynomial time complexity and shows much promise for its practical use. Experimental results are presented for a fairly representative benchmark of real-world data. Our test graphs include extracts of web-based social networks, including some very large ones, several well-known graphs from network science, as well as coappearance networks of literary works' characters from the DIMACS graph coloring benchmark. We also present results for synthetic pseudorandom graphs structured according to the Erdös-Renyi model and Leighton's model

Partitioning networks into cliques: a randomized heuristic approach

In the context of community detection in social networks, the term community can be grounded in the strict way that simply everybody should know each other within the community. We consider the corresponding community detection problem. We search for a partitioning of a network into the minimum number of non-overlapping cliques, such that the cliques cover all vertices. This problem is called the clique covering problem (CCP) and is one of the classical NP-hard problems. For CCP, we propose a randomized heuristic approach. To construct a high quality solution to CCP, we present an iterated greedy (IG) algorithm. IG can also be combined with a heuristic used to determine how far the algorithm is from the optimum in the worst case. Randomized local search (RLS) for maximum independent set was proposed to find such a bound. The experimental results of IG and the bounds obtained by RLS indicate that IG is a very suitable technique for solving CCP in real-world graphs. In addition, we summarize our basic rigorous results, which were developed for analysis of IG and understanding of its behavior on several relevant graph classes

On combinatorial optimisation in analysis of protein-protein interaction and protein folding networks

Abstract: Protein-protein interaction networks and protein folding networks represent prominent research topics at the intersection of bioinformatics and network science. In this paper, we present a study of these networks from combinatorial optimisation point of view. Using a combination of classical heuristics and stochastic optimisation techniques, we were able to identify several interesting combinatorial properties of biological networks of the COSIN project. We obtained optimal or near-optimal solutions to maximum clique and chromatic number problems for these networks. We also explore patterns of both non-overlapping and overlapping cliques in these networks. Optimal or near-optimal solutions to partitioning of these networks into non-overlapping cliques and to maximum independent set problem were discovered. Maximal cliques are explored by enumerative techniques. Domination in these networks is briefly studied, too. Applications and extensions of our findings are discussed

GraphCombEx: A Software Tool for Exploration of Combinatorial Optimisation Properties of Large Graphs

We present a prototype of a software tool for exploration of multiple combinatorial optimisation problems in large real-world and synthetic complex networks. Our tool, called GraphCombEx (an acronym of Graph Combinatorial Explorer), provides a unified framework for scalable computation and presentation of high-quality suboptimal solutions and bounds for a number of widely studied combinatorial optimisation problems. Efficient representation and applicability to large-scale graphs and complex networks are particularly considered in its design. The problems currently supported include maximum clique, graph colouring, maximum independent set, minimum vertex clique covering, minimum dominating set, as well as the longest simple cycle problem. Suboptimal solutions and intervals for optimal objective values are estimated using scalable heuristics. The tool is designed with extensibility in mind, with the view of further problems and both new fast and high-performance heuristics to be added in the future. GraphCombEx has already been successfully used as a support tool in a number of recent research studies using combinatorial optimisation to analyse complex networks, indicating its promise as a research software tool

Stochastic Analysis of a Churn-Tolerant Structured Peer-to-Peer Scheme

We present and analyze a simple and general scheme to build a churn (fault)-tolerant structured Peer-to-Peer (P2P) network. Our scheme shows how to "convert" a static network into a dynamic distributed hash table(DHT)-based P2P network such that all the good properties of the static network are guaranteed with high probability (w.h.p). Applying our scheme to a cube-connected cycles network, for example, yields a $O(\log N)$ degree connected network, in which every search succeeds in $O(\log N)$ hops w.h.p., using $O(\log N)$ messages, where $N$ is the expected stable network size. Our scheme has an constant storage overhead (the number of nodes responsible for servicing a data item) and an $O(\log N)$ overhead (messages and time) per insertion and essentially no overhead for deletions. All these bounds are essentially optimal. While DHT schemes with similar guarantees are already known in the literature, this work is new in the following aspects: (1) It presents a rigorous mathematical analysis of the scheme under a general stochastic model of churn and shows the above guarantees; (2) The theoretical analysis is complemented by a simulation-based analysis that validates the asymptotic bounds even in moderately sized networks and also studies performance under changing stable network size; (3) The presented scheme seems especially suitable for maintaining dynamic structures under churn efficiently. In particular, we show that a spanning tree of low diameter can be efficiently maintained in constant time and logarithmic number of messages per insertion or deletion w.h.p. Keywords: P2P Network, DHT Scheme, Churn, Dynamic Spanning Tree, Stochastic Analysis

Analysis of an iterated greedy heuristic for vertex clique covering

The aim of the vertex clique covering problem (CCP) is to cover the vertices of a graph with as few cliques as possible. We analyse the iterated greedy (IG) algorithm for CCP, which was previously shown to provide strong empirical results for real-world networks. It is demonstrated how the techniques of analysis for randomised search heuristics can be applied to IG, and several practically relevant results are obtained. We show that for triangle-free graphs, IG solves CCP optimally in expected polynomial time. Secondly, we show that IG finds the optimum for CCP in a specific case of sparse random graphs in expected polynomial time with high probability. For Baraba´si-Albert model of scale-free networks, which is a canonical model explaining the growth of social, biological or computer networks, we obtain that IG obtains an asymptotically optimal approximation in polynomial time in expectation. Last but not least, we propose a slightly modified variant of IG, which guarantees expected polynomial-time convergence to the optimum for graphs with non-overlapping triangles